Scale bar measurements and pixel sizes of mouse brain images

From your screenshot I can see you are referring to 2008 version of the Allen Reference Atlas.
This set of images has included as reference to the 2008 published book atlas.
You are correct it appears that the image resolution has not been set correctly.

For your project, I would recommend using a newer a version of the atlases listed in this page
Allen Reference Atlases :: Atlas Viewer (brain-map.org)

In particular consider using the Allen Mouse Common Coordinate Framework which is in active use and development.

Allen Mouse CCF - accessing and using related data and tools - Technical - Allen Brain Map Community Forum (brain-map.org)

The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas - PubMed (nih.gov)